The approach to highlighting HQs and sub-units is hard-coded in the game, I believe.
The best option (based on personal taste) is to edit the HQs so that:
1. They use bolder colours.
2. All Corps within the same Army use the same colour.
This way, as in the example, you can more easily spot where a particular Army's units are, while the Corp highlight puts a box around all sub-units in the Corp, allowing you to distinguish these from the rest of the army.
Not perfect, but probably better than the rainbow effect, IMHO.
I also moved the air units to OKH, for more clarity, but I am not sure what effect that has. I might add some Luftwaffe HQs in the campaign Willie Pete and I are modding together.